You need a payroll calculation set up as an after tax deduction.  The issue here is that you only get one account to credit.  So you either have to create multiple deductions, or you create a receivable account called employee purchases, set to use subaccounts.  Then on the payroll calculation you check the box to use employee # as subaccount number. 

CRITICAL:  When you enter the invoice that the company paid, it should be coded to that receivable account and create the subaccount for that employee using their employee # from payroll.  Because that is not an expense of the company, it should not be booked as such.  Now you have the amount paid on behalf of the employee and then the deductions taken until that debt has been reimbursed in full.  

You need a payroll calculation set up as an after tax deduction.  The issue here is that you only get one account to credit.  So you either have to create multiple deductions, or you create a receivable account called employee purchases, set to use subaccounts.  Then on the payroll calculation you check the box to use employee # as subaccount number. 

CRITICAL:  When you enter the invoice that the company paid, it should be coded to that receivable account and create the subaccount for that employee using their employee # from payroll.  Because that is not an expense of the company, it should not be booked as such.  Now you have the amount paid on behalf of the employee and then the deductions taken until that debt has been reimbursed in full.